Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm

ppiGReMLIN: a graph mining based detection of conserved structural arrangements in protein-protein interfaces

(2020) Felippe C. Queiroz et al.   BMC BIOINFORMATICS

Peptide-like and small-molecule inhibitors against Covid-19

(2020) Suyash Pant et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges

(2019) Alexander A. Vinogradov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Comprehensive Review on Current Advances in Peptide Drug Development and Design

(2019) Andy Chi-Lung Lee et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Metadynamics-Based Protocol for the Determination of GPCR-Ligand Binding Modes

(2019) Christian A. Söldner et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Pep‐Lipid Cubosomes and Vesicles Compartmentalized by Micelles from Self‐Assembly of Multiple Neuroprotective Building Blocks Including a Large Peptide Hormone PACAP‐DHA

(2019) Angelina Angelova et al.   ChemNanoMat

PepPro: A Nonredundant Structure Data Set for Benchmarking Peptide–Protein Computational Docking

(2019) Xianjin Xu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PepBDB: a comprehensive structural database of biological peptide-protein interactions

(2018) Zeyu Wen et al.   BIOINFORMATICS

Therapeutic peptides: Historical perspectives, current development trends, and future directions

(2018) Jolene L. Lau et al.   BIOORGANIC & MEDICINAL CHEMISTRY

StraPep: a structure database of bioactive peptides

(2018) Jian Wang et al.   Database-The Journal of Biological Databases and Curation

Protease inhibitory, insecticidal and deterrent effects of the trypsin-inhibitor benzamidine on the velvetbean caterpillar in soybean

(2018) ANDERSON M. PILON et al.   ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS

PixelDB: Protein-peptide complexes annotated with structural conservation of the peptide binding mode

(2017) Vincent Frappier et al.   PROTEIN SCIENCE

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Exploring the unbinding ofLeishmania(L.)amazonensisCPB derived-epitopes from H2 MHC class I proteins

(2016) Artur M. L. Brandt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

APD3: the antimicrobial peptide database as a tool for research and education

(2015) Guangshun Wang et al.   NUCLEIC ACIDS RESEARCH

Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms

(2014) Andrea Cavalli et al.   ACCOUNTS OF CHEMICAL RESEARCH

3Dmol.js: molecular visualization with WebGL

(2014) N. Rego et al.   BIOINFORMATICS

Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides

(2013) Ankur Gautam et al.   NUCLEIC ACIDS RESEARCH

PepBind: A Comprehensive Database and Computational Tool for Analysis of Protein–peptide Interactions

(2013) Arindam Atanu Das et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

CPPsite: a curated database of cell penetrating peptides

(2012) A. Gautam et al.   Database-The Journal of Biological Databases and Curation

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

(2011) George R Bickerton et al.   BMC BIOINFORMATICS

Survival and developmental impairment induced by the trypsin inhibitor bis-benzamidine in the velvetbean caterpillar (Anticarsia gemmatalis)

(2011) L.F. Moreira et al.   CROP PROTECTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment

(2010) Janez Konc et al.   BIOINFORMATICS

Structural basis of substrate specificity in the serine proteases

(2010) John J. Perona et al.   PROTEIN SCIENCE

Sub-angstrom modeling of complexes between flexible peptides and globular proteins

(2010) Barak Raveh et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Structural Basis of Peptide-Protein Binding Strategies

(2010) Nir London et al.   STRUCTURE

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

PepX: a structural database of non-redundant protein–peptide complexes

(2009) Peter Vanhee et al.   NUCLEIC ACIDS RESEARCH

MEROPS: the peptidase database

(2009) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Serine peptidases: Classification, structure and function

(2008) M. J. Page et al.   CELLULAR AND MOLECULAR LIFE SCIENCES